LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# SRD viscosity demo - poydisperse spheres

units           lj
atom_style      sphere
atom_modify     first big
dimension       2

# create big particles with 3 different types and diameters

lattice         sq 0.3
Lattice spacing in x,y,z = 1.8257419 1.8257419 1.8257419
region          box block 0 10 0 10 -0.5 0.5
create_box      4 box
Created orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
  2 by 2 by 1 MPI processor grid
create_atoms    1 region box
Created 100 atoms
  using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
  create_atoms CPU = 0.000 seconds

group           big type 1
100 atoms in group big
set             group big type/fraction 2 0.33 394895
Setting atom values ...
  35 settings made for type/fraction
set             group big type/fraction 3 0.5 989894
Setting atom values ...
  57 settings made for type/fraction
group           big type 2 3
100 atoms in group big

set             type 1*3 mass 1.0
Setting atom values ...
  100 settings made for mass
velocity        big create 1.44 87287 loop geom

# equilibrate big particles, repulsive only to prevent aggregation

pair_style      lj/cut 1.12
pair_coeff      1 1 1.0 1.0 1.12
pair_coeff      2 2 1.0 2.0 2.24
pair_coeff      3 3 1.0 1.5 1.68
pair_coeff      4 4 0.0 1.0 0.0

neighbor        0.3 bin
neigh_modify    delay 0 every 1 check yes

fix             1 big nve
fix             2 all enforce2d

#dump           1 all atom 10 dump.poly.equil

run             1000
Generated 6 of 6 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.54
  ghost atom cutoff = 2.54
  binsize = 1.27, bins = 15 15 2
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.172 | 4.172 | 4.172 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   1.44          -0.16013916     0              1.2654608      1.1298975    
      1000   1.3367862     -0.30816328     0              1.0152551      1.5440006    
Loop time of 0.00883083 on 4 procs for 1000 steps with 100 atoms

Performance: 48919544.759 tau/day, 113239.687 timesteps/s, 11.324 Matom-step/s
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.00040021 | 0.00044336 | 0.00050371 |   0.0 |  5.02
Neigh   | 0.00033682 | 0.00036617 | 0.00038566 |   0.0 |  4.15
Comm    | 0.006519   | 0.0065578  | 0.0066015  |   0.0 | 74.26
Output  | 1.1215e-05 | 1.2252e-05 | 1.4089e-05 |   0.0 |  0.14
Modify  | 0.00043326 | 0.00044482 | 0.00046058 |   0.0 |  5.04
Other   |            | 0.001006   |            |       | 11.40

Nlocal:             25 ave          29 max          23 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost:          33.75 ave          35 max          31 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Neighs:             38 ave          46 max          34 min
Histogram: 1 2 0 0 0 0 0 0 0 1

Total # of neighbors = 152
Ave neighs/atom = 1.52
Neighbor list builds = 115
Dangerous builds = 0

#undump         1
unfix           1
unfix           2

# add small particles as hi density lattice

region          plane block INF INF INF INF -0.001 0.001 units box
lattice         sq 250.0
Lattice spacing in x,y,z = 0.063245553 0.063245553 0.063245553
create_atoms    4 region plane
Created 83521 atoms
  using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
  create_atoms CPU = 0.006 seconds

set             type 4 mass 0.1
Setting atom values ...
  83521 settings made for mass
group           small type 4
83521 atoms in group small
velocity        small create 1.0 593849 loop geom

# delete overlaps
# must set *-4 cutoffs to non-zero values

pair_style      lj/cut 2.5
pair_coeff      1 1 1.0 1.0
pair_coeff      2 2 1.0 2.0
pair_coeff      3 3 1.0 1.5
pair_coeff      1 4 0.0 1.0 0.5
pair_coeff      2 4 0.0 1.0 1.0
pair_coeff      3 4 0.0 1.0 0.75
pair_coeff      4 4 0.0 1.0 0.0

delete_atoms    overlap 1.0 small big
System init for delete_atoms ...
Generated 3 of 6 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 14 14 2
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) command delete_atoms, occasional
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/2d
      bin: standard
  (2) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d
      bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
Deleted 63410 atoms, new total = 20211

# SRD run

reset_timestep  0

neighbor        0.3 multi
neigh_modify    delay 0 every 1 check yes

comm_modify     mode multi group big vel yes
neigh_modify    include big

# no pairwise interactions with small particles

pair_style      lj/cut 1.12
pair_coeff      1 1 1.0 1.0 1.12
pair_coeff      2 2 1.0 2.0 2.24
pair_coeff      3 3 1.0 1.5 1.68
pair_coeff      4 4 0.0 1.0 0.0

# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles

timestep        0.001

fix             1 big nve
fix             2 small srd 20 big 1.0 0.25 49894 shift yes 54979                   search 0.2 inside ignore
fix             3 small viscosity 10 x y 50
fix             4 all enforce2d

# diagnostics

compute         tbig big temp/sphere
variable        pebig equal pe*atoms/count(big)
variable        ebig equal etotal*atoms/count(big)
thermo_style    custom step temp f_2[8] etotal v_pebig v_ebig press                 f_2[1] f_2[2] f_2[3] f_2[4] f_2[5]                 f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]

thermo_modify   temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
thermo          1000

#dump           1 all atom 500 dump.poly.mp

#dump           1 all image 500 image.*.jpg type type zoom 1.6
#dump_modify    1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1

run             10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2

@Article{Intveld08,
 author =  {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
 title =   {Accurate and Efficient Methods for Modeling Colloidal
            Mixtures in an Explicit Solvent using Molecular Dynamics},
 journal = {Comput.\ Phys.\ Commut.},
 year =    2008,
 volume =  179,
 pages =   {320--329}
}

@article{Shire2020,
 author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
 title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
          Detection Applied to Investigate the Quasi-Static Limit},
 journal = {Computational Particle Mechanics},
 year = {2020}
@article{Monti2022,
 author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava, 
           Ishan and Silbert, Leonardo E. and Grest, Gary S. 
           and Lechman, Jeremy B.},
 title = {Large-scale frictionless jamming with power-law particle 
          size distributions},
 journal = {Phys. Rev. E},
 volume = {106}
 issue = {3}
 year = {2022}
}

- fix srd command: doi:10.1063/1.3419070

@Article{Petersen10,
 author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
 G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
 title =   {Mesoscale Hydrodynamics via Stochastic Rotation
    Dynamics: Comparison with {L}ennard-{J}ones Fluid},
 journal = {J.~Chem.\ Phys.},
 year =    2010,
 volume =  132,
 pages =   174106
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 3 of 6 mixed pair_coeff terms from geometric mixing rule
SRD info:
  SRD/big particles = 20111 100
  big particle diameter max/min = 1 1
  SRD temperature & lamda = 1 0.063245553
  SRD max distance & max velocity = 0.25298221 12.649111
  SRD grid counts: 73 73 1
  SRD grid size: request, actual (xyz) = 0.25, 0.25010162 0.25010162 1.8257419
  SRD per actual grid cell = 4.9371727
  SRD viscosity = 0.23321983
  big/SRD mass density ratio = 0.16131131
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
  # of rescaled SRD velocities = 0
  ave/max small velocity = 4.1934421 7.74495
  ave/max big velocity = 1.4399093 3.5724039
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.54
  ghost atom cutoff = 2.54
  binsize = 18.257419, bins = 1 1 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/multi/atomonly/newton
      stencil: half/multi/2d
      bin: multi
Per MPI rank memory allocation (min/avg/max) = 19.17 | 19.17 | 19.18 Mbytes
   Step          Temp          f_2[8]         TotEng        v_pebig         v_ebig         Press          f_2[1]         f_2[2]         f_2[3]         f_2[4]         f_2[5]         f_2[6]         f_2[7]         f_2[8]         f_2[9]        f_2[10]        f_2[11]    
         0   0.88820023     0              0.0050232797  -0.30816328     1.0152551      1.5440006      0              0              0              0              0              0              0              0              0              0              0            
      1000   0.83735494     3964           0.0071370659   0.19481352     1.4424724      3.9770741      7472           25             25             0              603            25600          5329           3964           0.96475118     0              2            
      2000   0.89694821     3981           0.0057098818  -0.18242861     1.1540242      3.1251883      7672           28             28             0              1238           25600          5329           3981           1.0589985      0              2            
      3000   0.99778172     3975           0.0051822049  -0.43931933     1.0473754      1.8970896      7814           24             24             0              1968           25600          5329           3975           1.1192504      0              3            
      4000   0.90067439     4030           0.0045096255  -0.43056442     0.91144042     1.8769981      8104           33             33             0              2911           25600          5329           4030           1.1382082      0              3            
      5000   0.90625848     4018           0.0055622776  -0.22613322     1.1241919      2.1866405      8287           26             26             0              3900           25600          5329           4018           1.1429442      0              3            
      6000   1.1284139      4022           0.0065653291  -0.354418       1.3269187      2.0312152      8268           35             35             0              5013           25600          5329           4022           1.1559733      0              3            
      7000   1.0073477      4043           0.0063924548  -0.2089691      1.291979       2.3332058      8433           39             39             0              6093           25600          5329           4043           1.1308958      0              3            
      8000   1.0621801      4050           0.00731979    -0.10324558     1.4794028      2.6610716      8353           40             40             0              7194           25600          5329           4050           1.1539521      0              3            
      9000   1.3173319      4046           0.0085268497  -0.23946297     1.7233616      2.4074596      8290           33             33             0              8498           25600          5329           4046           1.1601502      0              3            
     10000   1.1754738      4009           0.0074264713  -0.25049186     1.5009641      2.4237351      8305           30             30             0              9811           25600          5329           4009           1.1489476      0              43           
Loop time of 1.85719 on 4 procs for 10000 steps with 20211 atoms

Performance: 465218.852 tau/day, 5384.477 timesteps/s, 108.826 Matom-step/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0056791  | 0.0069765  | 0.0089852  |   1.6 |  0.38
Neigh   | 0.006991   | 0.0073805  | 0.0079507  |   0.4 |  0.40
Comm    | 0.10756    | 0.10836    | 0.10942    |   0.2 |  5.83
Output  | 0.00052479 | 0.0005511  | 0.00062567 |   0.0 |  0.03
Modify  | 1.6443     | 1.6772     | 1.7031     |   1.7 | 90.31
Other   |            | 0.0567     |            |       |  3.05

Nlocal:        5052.75 ave        5381 max        4651 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Nghost:           28.5 ave          30 max          26 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Neighs:          34.75 ave          55 max          26 min
Histogram: 2 0 1 0 0 0 0 0 0 1

Total # of neighbors = 139
Ave neighs/atom = 0.006877443
Neighbor list builds = 501
Dangerous builds = 0
Total wall time: 0:00:03
